Alignment
by Raven Ariana
Summary: Five years ago, Shirahane Yukina's only goal was to be reunited with Kennosuke. With her goal so close to being achieved, however, her mission becomes bigger than a reunion - and she must bring more than herself to Kennosuke if they are to stand any chance at all against the Efi Dolgs. Continuation fic. KenxYukina
1. Prologue

_Hi guys! So I'm back... after three years hiatus. Chapter 3 of Protected is still sitting half-finished in my folders. I'm so sorry!_

 _I've recently finished Kuromukuro's Season 2... and had had_ _ **had**_ _to DO something about that cliffy the moment I realised that Season 3 was not obviously forthcoming. So here goes my take on how the story continues, because the show MUST go on. I'll aim to have new chapters up each week. I have also acquired a new beta reader in the form of my best friend, whom I'm trying my best to convert into a fanfiction reader, hence my motivation._

 _Enjoy. I have included some story notes at the end of this prologue._

 _Disclaimer: Kuromukuro does not belong to me._

* * *

 _:Prologue:_

"I object to Shirahane- _san_ taking the _Medusa_ geoframe on this mission. Our forces against extraterrestrial invasion are limited as it is! We cannot be giving away Artifacts to forces whose allegiance to us is tentative at best." Carrie Dunham, the representative of the UN's Extraterrestrial Research Division and the biggest pain up Shirahane Hiromi's arse since the very first day she stepped into the Director's research institute, spoke up – just as the Chi-1 Sagittarius Assist Team's final meeting was about to be concluded.

Colonel Arthur Graham pinched the bridge of his nose and sighed, leaning heavily on his elbows against the hardwood desk. He had _really_ rather not have to re-hash this argument, after nearly six months spent convincing the UN and NATO leaders that this was a necessary move, but bureaucracy excelled at rearing its ugly head each time he thought he was done with it. Hiromi glanced at him and made the reply on his behalf, understanding that his patience was a rather thin line at the moment.

"Ms Dunham, I understand your concerns, but the plans have been cleared with all the leaders concerned, and _are final_. And to clarify, neither are we 'giving away' any assets, as the geoframes accompanying the mission will be piloted by our team members."

"And I suppose we are to believe that your daughter will not be handing _Medusa_ over to the extraterrestrial, Muetta, once she has a chance to co-pilot with her lover once again?"

"Her daughter is sitting right here, Ms Dunham, and would appreciate it if you would kindly address such concerns to her face," Yukina spoke up, turquoise eyes sharp as she met the gaze of the lady sat diagonally across from her. "May I remind you that this is a _military_ operation aiming to foster inter-stellar co-operation, and co-operation cannot be achieved where trust is not offered. We cannot continue to hoard resources and remain insular in the name of fear disguised as self-defense, not when the Efi Dolg are a threat to all, not just Earth."

Sophie met Hiromi's gaze and both smiled with pride at Yukina's level-headed, measured response. They had watched her grow, these five years, from a girl with conviction to a woman with conviction, and the skills to back it up. The Yukina of five years ago would have been able to make these arguments – in a shy, uncertain voice. The Yukina now knew what she wanted and what she was worth.

"The Extraterrestrial Research Division believes that there is more research to be done on these geoframes – " Ms Dunham frowned at Yukina for speaking out of turn, when she had been addressing Colonel Graham and Director Shirahane.

"And the Director will tell you that the institute has extracted all possible information from _Medusa_. Of course, if more information is required, _Long Arm_ , _Lockhead,_ and the restored _Blue Bird_ should provide more than sufficient material for research and will remain as Earth's defense," Yukina countered.

"Alongside the new GAUS units we have built, using the data gathered from these geoframes," Hiromi added. The UN had restored her as the Director of the Kurobe Research Institute, realizing that no one else was more qualified for the task when Hiromi's successor had been unable to catch up with her research notes after six months in the job. It was a great relief to her family – Hiromi and domesticity simply did not suit – and she had been able to lead the institute to develop fifty more GAUS units adapting the unique characteristics of the enemy geoframes.

"Very well," Ms Dunham conceded the point after a long silence. "We will relent as long as our division continues to have custody of the Efi Dolg, Yoruba, and further research on the Efi Dolg geoframes is shared. But you are very quiet, Colonel Graham. On what authority is Shirahane- _san_ answering all these questions?"

Colonel Graham, Director Shirahane, Yukina, Sophie, Sebastian, and the team members soon to be deployed in the Kurobe Survey Space Shuttle One began quietly packing their things at this sign that the meeting was winding down. Her loss of the argument rather irked the blonde-haired woman. Humans had opposed the idea of these extraterrestrials as allies for _years,_ and rightly so - they were an unknown quantity. Yet, so many of her compatriots had been swayed by this ragtag group of children and their far-fetched ideals, to the point where Earth was actually sending them to an unknown planet, swallowing resources that would have been better utilised on Earth's defense. _Plus_ , _I'm not sure we aren't sending them to certain death._ She scrutinised the lavender-haired young woman who had been surprisingly outspoken compared to the one she'd met five years ago.

Yukina tucked her tablet and notebook into the crook of her arm as she stood from her seat, ready to reveal something that had yet to be announced to the public – although, surely, many had guessed at it. "I," she said steadily, meeting Ms Dunham's gaze, "am Captain Shirahane Yukina, Commander of Kurobe Survey Space Shuttle One, and leader of the Chi-1 Sagittarius Assist mission. Thank you for voicing your concerns. This meeting is dismissed."

* * *

 _Ending Notes:_

 _I have made some assumptions about what happened during the five years prior to Yukina's departure for Chi 1 Sagittarius, which I will explain below (if they are not already explained in the story itself)._

 _\- That Major Arthur Graham has been promoted to Colonel, as he took charge of the isolated Kurobe Dam area after the Efi Dolg invasion._

 _\- That Shirahane Hiromi was reinstated as Director of the Kurobe Research Institute, because I think she must have been a combination of a genius and a good leader to have been appointed in the first place - although I am thinking this would have happened after the uproar over the Kurobe Incident died down._

 _\- My assumptions on the surviving, functional geoframes/grongols are based on whether or not their pilots were alive at the end of the final battle, as the geoframes' recovery appears to be tied to their pilots' recovery. We know Tom and Shenmei piloted Longarm to try and stop the Kuromukuro leaving Earth, so that's definitely functional, but I assumed that Blue Bird and Lockhead recovered as their pilots were kept in Earth's custody after they were defeated._

 _\- I will be referring to the geoframes/grongols as 'geoframes', as that was the humans' term for it. Of course, any Efi Dolg characters will refer to them as 'grongols'._

 _I welcome any constructive feedback - let me know what you think, or if I've made a factual error in the story!_

 _Until next time,_

 _Rave-chan._


	2. Chapter 1: Doubt

_The next chapter, as promised! Enjoy!_

* * *

\- I –

Doubts

Shirahane Yukina's turquoise orbs scanned the sleek, gleaming form of Kurobe Survey Space Shuttle One, affectionately nicknamed 'Taser' by the team soon to pilot it due to the two prongs stretching out and curving around the shuttle's propulsion engines. She was observing the ant-sized mechanics hurrying around the shuttle with their tools and checklists, conducting the final pre-launch checks, from the comfort of the rooms provided for her at the Toyama Spaceport. While she hadn't used these rooms frequently – she much preferred the simplicity and coziness of her family home – Yukina had to admit that the floor-to-ceiling windows afforded a glorious view of the spaceport grounds at dusk, with the runway lights glowing in uniform lines soothing the side of her that liked things neat and orderly.

The shuttle itself was the product of five years of dedication and collaboration between specialists worldwide. Director Hiromi's team at Kurobe Research Facility had provided the knowledge gained from experimentation with the Efi Dolg geoframes and Artifacts, while a team from NASA provided the aeronautics and space exploration expertise, and NATO contributed towards the defensive and offensive specifications of the spacecraft dominating the Toyama Spaceport's airfield. Meanwhile, all three organizations had contributed towards the intensive training (read: soul-sucking abyss of hell) Yukina and her team had undergone to prepare them for this mission.

There was a part of her that still couldn't believe it all. It had seemed like an impossibility five years ago, after that cruel separation from the man she had vowed to follow, after watching him leave with her replacement in the co-pilot seat of the geoframe she had begun to think of as _ours_ , while she was grounded far below, and couldn't follow. She had shouted that promise to the other half of her heart, held his own promise close as consolation, but after he was gone, her only thought was: _how am I going to do this?_ Who was going to help her, an eighteen-year-old high school girl with no qualifications except a few weeks spent piloting a giant mecha? It would've been far easier if she could've just followed him from the beginning!

She still hadn't quite forgiven Tom and Shenmei for that, if she was being perfectly honest.

And there was a part of her that wondered if – if – perhaps – Muetta had truly become her replacement. Yukina wasn't jealous by nature, but she had been eighteen, in love, and confused about it, and those few days during which Kennosuke had been so preoccupied with the Yuki- _hime_ -Muetta had hurt her in ways that she hadn't had the words to express. It didn't help that neither her nor Kennosuke had been particularly eloquent when trying to show how they felt – remembering his (unintentionally) public proposal still made her blush – and of course, she _knew_ how he felt, nobody who had heard the broadcast of their lovers' spat in the cockpit in those final moments could have doubted it (and she had replayed it thousands of times)… but still. It had been _five years_.

If – _when_ – they got to Sagittarius, would he even want here there?

"OW!"

Yukina spun around at the sudden, painful rap to the back of her head, one hand clutching the offended spot, the other whipping out to repay her attacker in kind, only to be blocked by a slim wrist held firm with surprising strength. Undeterred, Yukina let her arm slacken slightly, as if giving up on the offensive, before swiftly slipping past the block and tapping her attacker lightly on the forehead.

Sophie Nöel, Yukina's teammate and roommate at the Spaceport, did not even blink. Yukina knew that she'd only managed to touch Sophie because Sophie had allowed it, and allowed herself a small, sulky pout. Five years of intensive training had made her good at combat, but her abilities were still nothing compared to Sophie's natural aptitude and lifetime of training. But well. Yukina had outgrown sulking, and dropped the sour mood almost immediately.

"What was _that_ for, Sophie?" she demanded with no heat, turning back to the window.

Silence for a beat. Yukina could see Sophie observing her reflection in the glass, and wondered what her expression looked like to others.

"You are entertaining doubts again."

Yukina sighed and turned away from the window, neat lines of runway lights no longer providing comfort. She let herself flop down on her bed before replying.

"Yes, I am."

Yukina's eyes were trained on the ceiling, but she could hear Sophie's measured footsteps and felt her the mattress next to her dip as Sophie mirrored her position.

"And? Which one is it this time? Is it about Ms Dunham, your training, leaving your family, being not good enough to lead the mission, things going terribly wrong on the mission, another Efi Dolg invasion, things having gone wrong on Chi 1, or Kennosuke having replaced you after five years?"

The lavender-haired girl turned her head to glare at her roommate. Sophie merely met her gaze and raised an eyebrow. "Which one?"

"It's horrid that you know me better than I know myself," Yukina grumbled, throwing an arm over her eyes to shield herself from the suddenly-too-bright glare of the room lights – or perhaps it was Sophie's too-knowing gaze. She added, under the breath: "It's the last one."

"You're an idiot." Sophie's voice was blunt.

"And you could show some respect to your Commander."

"I would if you deserved it."

Damn, Sophie was giving no quarter today. Once upon a time Yukina had found her bluntness somewhat hostile and hurtful, but realized, after these five years, that it came from a kind place – besides, her best friend Mika had an equally blunt personality, only it was tempered by an exuberant personality that Sophie did not share.

"Just – humour me, and give me a little reassurance, would you?"

Sophie sighed that _you-are-exasperating_ sigh of hers, and sat up. Yukina felt a rather painful flick on her forehead moments later, as she expected, and did not counter.

"Ken is a _samurai_ , is he not?" Sophie demanded.

Yukina nodded once, her forearm still obscuring her eyes.

"And what is a _samurai_ 's most important trait?"

"Honour." Yukina mumbled. Sophie was turning full-on _samurai otaku_ on her.

"Well then. Did he or did he not say he wanted you to be his wife?"

"… the outcome of that was doubtful."

"That's a matter of perspective. Did he or did he not promise he would wait for you?"

"… he did."

"And a _samurai_ 's word is his honour, is it not?"

"I suppose so."

" _It is._ " Sophie deadpanned. "More so for Ken, who, like an idiot, was fixated on avenging and protecting the lookalike of a princess who died _four hundred and fifty-five_ years ago… because he promised to do it. Why would his promise to you be any different?"

"Because that was four hundred and fifty years during which he was unaware of the world! Because he has been alive and awake these five years, and we haven't even been able to _speak_ ," Yukina gritted out, eyes suddenly itching, even under the cover of her arms. "How could I expect him not to have changed?"

Before Sophie could reply, the automated doors to their room slid open, and Mika, Director Shirahane, and Koharu clattered in, full of chatter that halted the moment they spotted Yukina flopped on the bed, her mouth downturned.

Ogina Mika frowned, resting a hand on her cocked hip as she looked at Sophie with a long-suffering expression. Director Shirahane and Koharu glanced back and forth between them, looking thoroughly confused at their familiarity with this situation. "So. Is it about Ms Dunham, her training, leaving her family, being not good enough to lead the mission, things going terribly wrong on the mission, another Efi Dolg invasion, things having gone wrong on Chi 1, or Kennosuke having replaced her after five years, this time?"

"The last one," Sophie responded, arms and legs crossed as she perched gracefully on the edge of Yukina's bed.

All four women turned their gazes on Yukina's still-prone form, and chorused: "You're an _idiot_."

"Alright, alright already!" Yukina bolted upright, growling. "Stop ganging up on me and leave me to sulk in peace during my last night on Earth!"

"No can do," Mika responded matter-of-factly, striding over and grasping her best friend by the arm, tugging her up. "We're here to drag you to the launch party. No more sulking allowed." Director Shirahane and Koharu nodded along, each picking a part of her to pull along.

Something about the familiarity of this situation, the parallels between this and the way she had dragged Kennosuke along, been dragged along herself, the way they had forced each other to acknowledge hard truths, made Yukina's resolve tighten.

"Wait – wait. I can't go out there like this," Yukina forced them to a halt, five years of combat training and natural leadership coming through. She spotted the small smile forming at the corners of Sophie's mouth, and knew that she was going to be teased about this at some point… but never mind.

"I promised I would go to him, and he promised he would wait for me," she announced. The four women nodded, and Yukina absently thought that it was nice, for once, to have all of them agreeing on something. "I can't control, or know, what he does or how he feels," she added, earning herself some confused looks, "but I can fulfill my part of the bargain."

"And trust him to fulfill his," Sophie added quietly. "His word is his honour, _Commander,_ " There was a light in Sophie's amethyst eyes that spoke of respect, and all of Yukina's doubts lifted.

The lavender-haired woman gave herself a couple of firm pats on her cheeks, and straightened her uniform, looking around and meeting the gazes of the four women she loved and respected the most. "Alright then! Let's go have ourselves a launch party no-one will forget."

"Yes, Commander!"

* * *

 _I tried to explore what Yukina's thoughts and feelings might have been, considering the years that had passed and how difficult it must have been to achieve her goal of joining Kennosuke. The action will begin soon!_

 _Let me know what you think!_

 _Thanks,_

 _Rave-chan_


	3. Chapter 2: On the Other Side

_Thank you so much for all the reviews, follows, and favourites! They keep me going. Apologies for the delay - this chapter required a lot of world- and character- building, and I got pretty stuck for awhile! Thought it would be fun to find out how Kennosuke and the others were doing ;)_

 _Enjoy!_

* * *

 **-II-**

 **On the Other Side**

"Ken _,_ what is your status?"

Zell's voice crackled over Kennosuke's helmet's speakers as he dodged behind the frame of a hovercraft in the largest scrap-yard on Chi-1, avoiding detection by the battered cactus-bot left to patrol this wasteland on its own. Discarded Chi-1 technology and vehicles lay around him in dirty, dented piles, covered in the fine sand Kennosuke now knew to be characteristic of the land located near the glittering crater-lake of Chi-1. He waited a beat before answering.

"Only one cactus-bot observed patrolling. I am waiting for it to leave this section before I start my search."

"Noted. Do not get too close to the biodome surrounding the lake settlement. It may have more surveillance features installed."

Kennosuke's gaze darted towards the shimmering dome stretching over the crater-lake and the Efi Dolg mothership planted on the opposite shore – barely recognisable as such due to its permanent lodging on this planet. Gleaming extensions had been added under the mainframe, forming a strangely haphazard castle structure with a domed top that appeared hideous to him when compared to the beautiful white walls and slanted rooves of the castle he once served, or the cosy Shirahane home.

There was nothing left of the colourful nomad tents that once occupied the desert lands of Chi-1, described wistfully by Zell. It was close to the Eclipse, but there was no shimmering vapour rising from the lake either, as something in the Efi Dolg biodome interfered with the celestial event. The science had been explained by one of Zell's compatriots in their underground insurgent camp, but well, Kennosuke's head wasn't made for science. He _did_ understand the loss of beauty, though, and the significance of ripping away something people considered important, in demoralizing the enemy.

Kennosuke felt something twist in his chest at that thought. As a warrior, he had understood that concept, but until the moment he had been forced to leave Yukina behind, he had not been able to fathom just how hard the loss would hit him. That he had ever thought he would be able to leave Earth without her was laughable. He would survive, he _needed_ to survive, but there was a light in his life that had dimmed considerably, a warmth that just wasn't there. And the uncertainty that she would ever be able to find him, join him…

Kennosuke shook his head to rid himself of unhelpful thoughts, and returned to the task. The cactus-bot had moved to patrol a section further up. Time to move.

"The area is clear. I will begin the search."

"Copy that. I am leaving the comm link to Voltra," Zell responded, speaking of a cheerful, young insurgent engineer from Base C-1, "he'll assist with identifying the parts. I will be meeting the leaders from C-2 and 3 to get an update on their recon and retrieval activities – if you see anything of note, tell Voltra to pass it on."

"Zell- _dono_." The samurai acknowledged the instruction with a murmur, dark eyes carefully scanning his surroundings, the warrior part of him on full alert, while the analytical part of him considered the information Zell had imparted.

Chi-1's insurgents, when Kennosuke, Muetta, and Zell had first landed, had been a motely crew of about twenty more concerned about survival than rebellion. But their expressions had changed from utter exhaustion to tentative hope when they set eyes on Zell and their geoframes.

Zell had quietly gathered more allies, ferreted out the pockets of his people who had managed to evade the clutches of the Efi-Dolg's brainwashing nano-machines, until their group had grown into a small force of two hundred, spread out amongst three underground camps with some semblance of organisation. C-1 was based in an old quartz mine near the crater-lake of Zell's memories, his former home; C-2 was a sprawling underground network buried beneath Chi-1's previous metropolis; while C-3 occupied a large cave system in a mountainous area. Now Zell was turning his attention towards rebuilding the technology of his people, discarded and replaced by the Efi Dolg who had not tried to understand systems different from their own.

Kennosuke eyed the barely-distinguishable piles of scraps heaped around him, and glanced at the complex diagrams of components the insurgent engineers required hovering on the left side of his helmet visor. He allowed himself a small sigh, and started his search.

* * *

"I remain of the opinion that it is time to make an attempt to breach at least _one_ of the Efi Dolg territories. The resistance is not on their radar – and we need to know more about their numbers, structure, and defenses if we are ever to retake Chi-1," Alia Sonder _Vishrai_ , leader of the C-2 base and one of Zell's contemporaries before the invasion, tapped a long finger on the tabletop as she pushed her point, squarely meeting the gazes of others in the Council of Nine – comprised of the three Base Leaders and a rotation of two members from each base, every meeting.

"The risk is still too high," Zell frowned, looking thoughtfully at the holo-map of the Chi-1 territories floating above the table, with its glowing info-bubbles containing the most up-to-date intel the insurgents had of the Efi Dolg territories. The invaders had conquered Chi-1 and left three of their motherships to hold their territory within separate biodomes across the planet, confining the infected natives within them to run the day-to-day operations. Cactus-bots ran surveillance outside the biodomes, but the insurgents had become so skilled at hiding that surveillance had gradually decreased to rudimentary levels, the Efi Dolg likely believing that all resistance had been crushed. But there was still too little information on the Efi Dolg command structure and territory within the biodomes – and research into the biodomes' structure and the possibility of breaching them was ongoing.

Alia turned towards the leader of C-3, a younger, yet charismatic, strategist during the pre-invasion era, named Hanrel Zusak _Manrai,_ with a questioning look. "Hanrel? Your thoughts?"

The strategist met her piercing gaze calmly. "I think we should not proceed until we are reasonably certain of success. As Zelleager _Vishrai_ said, the risk far outweighs the rewards. We are not ready. At the very least, we need a way to breach the biodomes without bringing the Efi Dolg fleet down on us. And as you pointed out, Alia _Vishrai_ , our resistance is not on their radar. That gives us time that we would otherwise not have, to ensure we are prepared before we make any moves that are likely to gain us unwanted attention."

"We also need allies," Zell weighed in, his tone heavy. "We cannot hope for any victories unless we have a force to counter the Efi Dolg's retaliation, once we are exposed." Zell thought wistfully of his Earthen allies, before turning to his assistants for this meeting: "Do we have any more leads on Zara Myundef's whereabouts?"

"We know that she left Sagittarius, Zelleager _Vishrai_ , but we have nothing more concrete beyond that."

"What about other communications?" Alia turned to her own assistants.

"We have sent out tentative probes, Alia _Vishrai,_ but our signals are affected by the Efi Dolg satellite scramblers."

Alia's expression was grim. "We are at an impasse, then," she addressed the Council.

"I suggest we focus efforts on supporting our engineers in developing ways to breach the biodomes and make contact with potential allies. Any plans beyond that would be based on conjecture," Hanrel responded, and Zell nodded.

Alia sighed. "Very well, then. Now, on to the question of supplies…"

* * *

"To your left, Ken- _san_ , under the set of black prongs – I see a crystal-powered generator," Voltra's cheerful voice sounded over Kennosuke's comm as he attempted to extract his left arm, which was elbow-deep in one pile of scrap metal in an attempt to reach what Voltra had thought was a radio antenna, but turned out to be a tent pole.

The samurai was hot, tired, and ready to toss Voltra and his cheerful voice into the lake at the next opportunity. An hour of fruitless searching had reinforced Kennosuke's initial opinion of this excursion – it was absurd to send _him_ looking for _technology_ , of all things, even if he was the strongest combatant in their base.

Swallowing the snarky retort forming on the tip of his tongue, Kennosuke turned to look in the direction Voltra had indicated. Helpfully, a red outline superimposed itself over the image of aforementioned piece on Kennosuke's visor as he turned his head. The outline matched perfectly. This might just work, after all, Kennosuke thought as he reached out.

"I have it," Kennosuke carefully extracted the generator from the pile and turned it over in his hands so that Voltra could confirm it was what they needed.

"We found it! I hope it's operational," Voltra's glee could be heard through the crackly comm line. "Ken- _san_ – I think I see a particle distorter under that frame to your right. You'll have to dig, though."

Kennosuke stowed the generator safely inside the bag he had been given, and proceeded towards the object outlined in red on his visor. It was under a pile close to the shimmering biodome, and he considered if the metal frame above the piece they wanted would support the weight of everything above it, if he pulled the particle distorter out of the pile.

"I'll have to pull it out," Kennosuke informed Voltra as he gripped the object, and eased it out carefully, watching the movement of the scraps above it. "… I think I have it." The frame supporting the rest of the pile held as Kennosuke pulled the particle distorter free.

"We're good!" Voltra crowed. "And if that particle distorter works, we might just make a breakthrough on the biodome breach research –"

Kennosuke was in the process of shoving the particle distorter into the bag, but he was no longer listening to Voltra, and was instead staring, wide-eyed, at the frame that was supposed to support the weight of the pile, buckling slowly inwards, and only recovered sufficiently to leap back as the entire heap of scraps collapsed in a thunderous crash, sending debris flying and smashing into the biodome, which rippled red from the point of contact – some sort of alarm? – and brought the unwelcome whirring of cactus-bots headed in the direction of the crash.

Allowing himself a second to swear, Kennosuke snatched up his bag and _ran_.

* * *

 _Notes:_

 _\- I took some liberties in making part of Zell's full name (Zelleager Myundef Vishrai) a title to indicate some sort of rank... so that I could invent new ones too!_

 _\- The insurgent bases are located near Efi Dolg holdings. I'm going to assume Chi-1 is a relatively small planet, because it makes world building marginally easier._

 _Tell me what you think - I love getting feedback!_

 _Until next time,_

 _Rave-chan_


End file.
